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Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

View ORCID ProfileSaif M. Khodary, View ORCID ProfileAli Mostafa Anwar
doi: https://doi.org/10.1101/2020.04.01.019463
Saif M. Khodary
1Department of Genetics, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
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Ali Mostafa Anwar
1Department of Genetics, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
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  • For correspondence: ali.mo.anwar@std.agr.cu.edu.eg
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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries) in an attempt to characterize it, unravel the main force shaping its pattern, and understand its adaptation to Homo sapiens. Overall results revealed that, SARS-CoV-2 codon usage is slightly biased similarly to other RNA viruses. Nucleotide and dinucleotide compositions displayed a bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Eight common putative preferred codons were identified, and all of them were A/U-ended (U-ended: 7, A-ended: 1). In addition, natural selection was found to be the main force structuring the codon usage pattern of SARS-CoV-2. However, mutation pressure and other factors such as compositional constraints and hydrophobicity had an undeniable contribution. Two adaptation indices were utilized and indicated that SARS-CoV-2 is moderately adapted to Homo sapiens compared to other human viruses. The outcome of this study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 and may aid in vaccine design strategies.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • A section on the materials and methods, as well as on the result were updated, to clarify, without changing any significant results from version 2.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 07, 2020.
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Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations
Saif M. Khodary, Ali Mostafa Anwar
bioRxiv 2020.04.01.019463; doi: https://doi.org/10.1101/2020.04.01.019463
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Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations
Saif M. Khodary, Ali Mostafa Anwar
bioRxiv 2020.04.01.019463; doi: https://doi.org/10.1101/2020.04.01.019463

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